Like the first green jacket episode, in Episode 7 of the Death Note dorama streaming on Crunchyroll, Light dresses like a janitor to sneak into a corporate building.
Update: In the fifth volume of Assassination Classroom, they got Koro-sensei paraphrasing Zenitagata's 'stole something precious' line from Cagliostro. In AC's case, though, they changed the object from 'your heart' to 'your tentacles'.

Update 2: The
second episode of Hokuto no Ken DD 2 has a clocktower gag reminiscent of Cagliostro.
Update 3: DD Fist of the North Star II has a reference to Heiji Zenigata, Pops' ancestor.
Update 4: This is stretching it, but Girls and Panzer 'homage' to
Cagliostro.
Update 5: This is technically an old Lupin reference in the new Lupin, but if you check out the background of the ball of blue jacket 22, you'll notice the bad guy from the Miyazaki episode Wings of Albatross is there.